Hi,
Recently I tried to generate a RNA topology by martinize-nucleopeptide.py script.
I followed every step that is listed in the RNA tutorial for my RNA sequence but the final structure of the cg RNA is not match with the All Atom structure at the both end of the RNA.
As you can see in the provided image, there are two bases on the top and one in the bottom that are not coarse grained.
Image LINK
Seems strange, could you please hep me find a solution for that?

When martinize-nucleotide.py generates two .itp files it usually means there is something strange in the atomistic .gro file. If you are using only standard residues, make sure all residues are named like DX (e.g. DA, DC, DG, DT).

If the problem persists, try to use the atomistic .pdb with tleap (a module in Ambertools). With this you will make sure the order and the name of the atoms is correct. If you have questions on which commands to run tleap, send me an email to This email address is being protected from spambots. You need JavaScript enabled to view it..